Telluride Workshop on
The Complexity of Dynamics and Kinetics in Many Dimensions


From Braidal Veil Trail in Telluride.  They are winding, aperiodic
but yet somewhat ordered (for a certain temporal period) to the goal,
reminiscent of what functions are in complex systems.

June 16-June 20 2013
Telluride Intermediate School
Telluride Summer Research Center
Telluride, CO, USA

 


 

 

This workshop focuses on the complexity of dynamics and kinetics in complex systems, such as proteins, in terms of the underlying multidimensional energy landscape, the network structure in the conformational, or, in general, state space, and various mathematical models of nature. We aim at having an interdisciplinary meeting that brings both theoretical and experimental researchers together from different fields including time series analysis, energy landscape, statistical physics, network analysis, and single molecule experiments.

This year, the main questions to be addressed are:


1. What are the current and next generation experimental advances to probe the dynamics and kinetics of complex biophysical systems, such as single molecule spectroscopy and microscopy, cell imaging, multi-parameter measurements, and what are the desired analysis methods to scrutinize the observed data?


2. What are the appropriate mathematical languages to model complex dynamics and kinetics from experiments or computer simulations, such as generalized Langevin equations, master equations, networks, disconnectivity graphs? How can the mathematical models be constructed from scalar, multivariate or imaging (spatiotemporal) data? For example, how to extract hidden dimensions, how to reduce dimensions?


3. What are the dynamical and thermodynamical signatures of the constructed models? The related subjects are, for example, diffusion properties, memory effects, the quantification of multiple pathways on the energy landscape and its relations to the protein structures, equilibrium and nonequilibrium properties.


4. If the constructed models are complicated, e.g. in the conformational-space network, how can the essential features be extracted and represented, such as coarse-grained models, quantifying the large scale structure of networks, identifying reaction coordinates and flux?

Notes:
This Telluride workshop is different from a traditional conference. This workshop is aimed at exploring the new, exciting, open questions, by stirring different disciplines working on different subjects and fields rather than solely to learn about all the wonderful things the participants have already done. Some of the most interesting Telluride workshops have used a format in which the first day or the half of the first day is devoted to setting an agenda of the open topics to be discussed, choosing who should be the formal presenter of each of those topics, and setting the day for each presentation. The material that would, in a traditional conference be presented in a talk, would have been contained in the pre-circulated papers. Then everyone will know the substance of where each subject stands and the focus can be on what needs to be investigated next, and how those things could be approached. We plan to follow this pattern, and will ask the participants to submit one or two papers that they would like the others to see, and to send us a list of the exciting, important open problems that they feel should be discussed at this workshop.

 

Participants

name

affiliation

arrival

departure

Berry, R. Stephen

University of Chicago, USA

9-Jun

20-Jun

Clementi, Cecilia

Rice University

15-Jun

20-Jun

Crutchfield, James

University of California, Davis

15-Jun

20-Jun

Green, Jason

University of Massachusetts - Boston

15-Jun

20-Jun

Henkelman, Graeme

University of Texas at Austin

13-Jun

20-Jun

Hernandez, Rigoberto

Georgia Institute of Technology

Li, Chun-Biu

Hokkaido University

15-Jun

20-Jun

Komatsuzaki, Tamiki

Hokkaido University

15-Jun

20-Jun

Marcus, Andrew

University of Oregon

16-Jun

20-Jun

Makarov, Dmitrii

University of Texas at Austin

15-Jun

20-Jun

Marsden, Annie

University of Chicago

16-Jun

21-Jun

Nagahata, Yutaka

Hokkaido University

15-Jun

20-Jun

Presse, Steve

Indiana University-Purdue University Indianapolis

15-Jun

20-Jun

Wang, Jin

Stony Brook University

16-Jun

20-Jun

Scherer, Norbert

University of Chicago

14-Jun

20-Jun

Teramoto, Hiroshi

Hokkaido University

15-Jun

21-Jun

Toda, Mikito

Nara Women’s University

Douglas, Jack

National Institute of Standards and Technology

 

Group picture

 

TSRC Complexity,June'13 copy.jpg

Picture taken in front of Telluride intermediate school (June 17th 2013).

Top row: Jin, Steve(Berry), Jim, Chun-Biu, Rigoberto, Cecilia, Tamiki

Bottom row: Yutaka, Norbert, Hiroshi, Jason, Mikito, Annie, Dmitrii, Steve(Presse), Andrew


Workshop dates and venue
The workshop will begin at 9:00 am on Sunday, June 16 and end at 12:00 pm on Thursday, June 20. The workshop will be held at the Telluride Intermediate School (see Map). Breakfast is served at the workshop location on Sunday-Thursday at 8:30 am and the talks start at 9:00 am. You will have access to the internet, faxes, express mail services, and so forth.



Tentative Program

 

Sun 6/16

Mon 6/17

Tue 6/18

Wed 6/19

Thu 6/20

8:30

Breakfast served at school from 8:30

9:00

Opening Remark, Set up Agenda

Presse, Li, Wang

Makarov, Marcus,
Green, Nagahata

Scherer,
Teramoto, Douglas

Open Discussion

9:30

Berry, Komatsuzaki,
?Crutchfield

10:00

10:30

11:00

11:30

Closing remarks

12:00

(Lunch) in school

(Lunch) in school

12:30

13:00

13:30

(free to be changed)

Hernandez, Cecilia
Henkelman, Toda

(free to be changed)

(free to be changed)

14:00

14:30

15:00

15:30

16:00

16:30

17:00

17:30

18:00

Sunday Reception at New Sheridan Bar

Group Dinner at Cosmo 300 W. San Juan

Town Talk at the Historic Opera House 110 N. Oak St.

Wed Night Picnic at the Ah Haa School 300 S. Townsend

18:30

19:00

19:30

20:00

20:30

 

 

Talk Titles

 

name

title

remarks

Berry, R. Stephen

Bridging the Micro-Macro Divide

A subject that has been considered a major unsolved issue, for which we've found a tool to address it.? We have applied it in only one case, the size boundary below which the Gibbs Phase Rule is inapplicable, but we see some other problems that could be addressed in analogous ways.

Clementi, Cecilia

Multiscale Modeling of Macromolecular Dyanmics

 

Crutchfield, James

Computation at the Nanoscale:? Some thoughts on information processing in novel materials, molecules, and atoms

I will review recent results on how to detect and measure information processing embedded in the behavior of nonlinear dynamical systems. Illustrations will be taken from closed-packed 1D materials and highly excited (Rydberg) atoms

Green, Jason

Signatures of thermodynamics far from equilibrium

 

Henkelman, Graeme

TBA

 

Hernandez, Rigoberto

Adaptive Steered Molecular Dynamics (ASMD): Unfolding of Neuropeptide Y and Decaalanine Stretching

 

Komatsuzaki, Tamiki

Revisiting Energy Landscape & Extracting it from FRET measurement

 

Li, Chun-Biu

Does Dynamic Disorder Exist in the Enzymatic Reactions on the Single Molecule Level?

 

Makarov, Dmitrii

The dynamics of unfolded proteins:? rough energy landscapes, memory, internal friction and what we can learn about them from single-molecule studies

 

Marcus, Andrew

Studies of DNA 'Breathing' and Helicase binding at Replication Fork Junctions by Single-Molecule FRET, Linear Dichroism, and Two-Dimensional Fluorescence Spectroscopy

 

Marsden, Annie

TBA

 

Nagahata, Yutaka

Identifying states in Markov chain steady state network extracted from time series by finding minimum transition probability

 

Presse, Steve

Determining the stoichiometry of protein complexes in situ from superresolution imaging data

OR

Inferring models from noisy data across multiple length scales: from single biomolecules to protein complexes

 

Scherer, Norbert

Nonequilibrium chemical cycles create a unit of time in a bacterium

 

Teramoto, Hiroshi

Coherent Dynamics in Colloidal Fluids in terms of Lagrangian Coherent Structure

 

Toda, Mikito

Analysis of motion features using wavelet for molecular dynamics simulation of proteins

A new method to extract nonstationary features of coarse grained motions is presented for time series data of molecular dynamics simulation of proteins. We use the wavelet transformation together with the singular value decomposition (SVD). The wavelet analysis enables us to characterize time varying features of the dynamics and SVD enables us to reduce the degrees of freedom of the data. We apply our method to time series data obtained by molecular dynamics simulation for Thermomyces lanuginosa lipase (TLL).

For TLL, by introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving disordered proteins

Wang, Jin

TBA

Douglas, Jack

Collective motion and relaxation in condensed materials

 

 


Registration

One can register the workshop via the following web page: http://www.telluridescience.org/registration
(This registration fee is for running our conference at Telluride Science Research Center (TSRC), including using computational facilities and breakfast (a huge variety including hard boiled eggs, ham, bread, pastries, bagels, cheese, juice, coffee, tea) during the workshop)



Telluride Tips & Frequently Asked Questions
please visit here and the travel tips page provided by Douglas J. Tobias.


Organizers

Tamiki Komatsuzaki
Molecule & Life Nonlinear Sciences Laboratory
Research Institute for Electronic Science
Hokkaido University
TEL&FAX +81(11) 706-9434
Email: tamiki@es.hokudai.ac.jp
http://mlns.es.hokudai.ac.jp/

R. Stephen Berry
Department of Chemistry, and the James-Franck Institute,
University of Chicago, USA
TEL +1-773-702-7021 FAX:+1-773-702-0805
E-mail: berry@uchicago.edu
http://chemistry.uchicago.edu/fac/berry.shtml

Chun-Biu Li
Molecule & Life Nonlinear Sciences Laboratory
Research Institute for Electronic Science
Hokkaido University
TEL&FAX +81(11) 706-9435
Email:cbli@es.hokudai.ac.jp
http://mlns.es.hokudai.ac.jp/index.html